Mercurial > repos > bgruening > 10x_bamtofastq
changeset 0:110076d77197 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 339363f6c9d817bc2c35997b4dfdd3ca99a37055
author | bgruening |
---|---|
date | Tue, 10 May 2022 12:02:15 +0000 |
parents | |
children | f71fd828c126 |
files | 10x_bamtofastq.xml test-data/A10.sub.bam test-data/bamtofastq_S1_L007_I1_001.fastq.gz test-data/bamtofastq_S1_L007_R1_001.fastq.gz test-data/bamtofastq_S1_L007_R2_001.fastq.gz |
diffstat | 5 files changed, 74 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/10x_bamtofastq.xml Tue May 10 12:02:15 2022 +0000 @@ -0,0 +1,74 @@ +<tool id="10x_bamtofastq" name="Convert a 10X BAM file to FASTQ" version="1.4.1"> + <requirements> + <requirement type="package" version="1.4.1">10x_bamtofastq</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + bamtofastq --nthreads "\${GALAXY_SLOTS:-4}" --reads-per-fastq 10000000000 + #if $convert.reads == 'subset': + --locus $convert.locus + #end if + $produced_from + $tenx_bam + outdir && + mv outdir/*/*.fastq.gz outdir + ]]></command> + <inputs> + <param format="bam" name="tenx_bam" type="data" label="10X Genomics BAM file to convert to FASTQ"/> + <conditional name="convert"> + <param name="reads" type="select" label="Read pairs to convert?"> + <option value="all">Complete BAM file</option> + <option value="subset">Only a subset of BAM file</option> + </param> + <when value="all" /> + <when value="subset"> + <param name="locus" type="text" value="" + label="Only include read pairs mapping to a locus." + help="The format is chr:start-end, for example "chr1:14300-125000"."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value=":"/> + <add value="-"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + <param name="sort" type="boolean" label="Skip unpaired or duplicated reads instead of throwing an error?" checked="False" falsevalue="" truevalue="--relaxed"/> + <param name="produced_from" type="select" label="BAM file produced from"> + <option value="">Long Ranger v2.1+ and Cell Ranger v1.2+</option> + <option value="--gemcode">GemCode data (Longranger 1.0 - 1.3)</option> + <option value="--lr20">Longranger 2.0</option> + <option value="--cr11">Cell Ranger 1.0-1.1</option> + </param> + </inputs> + <outputs> + <collection name="fastq_collection" type="list" label="10x FASTQs from ${on_string}"> + <discover_datasets pattern="(?P<designation>.+)\.fastq\.gz" directory="outdir" format="fastqsanger.gz"/> + </collection> + </outputs> + + <tests> + <test> + <param name="tenx_bam" value="A10.sub.bam"/> + <output_collection name="fastq_collection" type="list" count="3"> + <element name="bamtofastq_S1_L007_I1_001" file="bamtofastq_S1_L007_I1_001.fastq.gz"/> + <element name="bamtofastq_S1_L007_R1_001" file="bamtofastq_S1_L007_R1_001.fastq.gz"/> + <element name="bamtofastq_S1_L007_R2_001" file="bamtofastq_S1_L007_R2_001.fastq.gz"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ + 10x Genomics BAM to FASTQ converter + ]]></help> + <citations> + <citation type="bibtex"> + @misc{github10xbamtofastq, + author = {}, + year = {2022}, + title = {10x bamtofastq}, + publisher = {Github}, + journal = {Github repository}, + url = {https://github.com/10XGenomics/bamtofastq}, + }</citation> + </citations> +</tool>